1. Field of the Invention
The present invention relates generally to computerized analysis of genetic information via an internet portal, and particularly, but not exclusively, to computerized systems and methods for the analysis of genetic profiles. More particularly, but not exclusively, the present invention relates to computerized systems for paternity and maternity testing using genetic profiles.
2. Definitions
Internet: The network of networks and gateways that use the TCP/IP suite of protocols.
Client computer: A computer which issues commands to the server.
Server: Any computer that performs a task at the command of another computer is a server. A Web server typically supports one or more clients.
World Wide Web (WWW or Web): The Internet's application that lets people seeking information on the Internet switch from server to server and database to database by clicking on highlighted words or phrases of interest (hyperlinks). An Internet WWW server supports clients and provides information. The Web can be considered as the Internet with all of the resources addressed as URLs and which uses HTML to display the information corresponding to URLs and provide a point-and-click interface to other URLs.
Universal Resource Locator (URL): A way to uniquely identify or address information on the Internet. Can be considered to be a Web document version of an e-mail address. They can be accessed with a Hyperlink. An example of a URL is “http://www.edpbiotech.com.html”. A URL has four components. Starting from the left, the first specifies the protocol to use, separated from the rest of the locator by a “:”. Next is the hostname or IP address of the target host; this is delimited by the “//” on the left and on the right by a “/” or optionally a “:”. The port number is optional, and is delimited on the left from the hostname by a “:” and on the right by a “/”. The fourth component is the actual file name or program name. In this example, the “.html” extension means that this is an HTML file.
HyperText Markup Language (HTML): HTML is the language used by Web servers to create and connect documents that are viewed by Web clients. HTML uses Hypertext documents. Other uses of Hypertext documents are described in U.S. Pat. No. 5,204,947, granted Apr. 20, 1993 to Bernstein et al.; U.S. Pat. No. 5,297,249, granted Mar. 22, 1994 to Bernstein et al.; U.S. Pat. No. 5,355,472, granted Oct. 11, 1994 to Lewis; all of which are assigned to International Business Machines Corporation, and which are incorporated by reference herein.
Hypertext Transfer Protocol (HTTP): HTTP is an example of a stateless protocol, which means that every request from a client to a server is treated independently. The server has no record of previous connections. At the beginning of a URL, “http:” indicates the file contains hyperlinks.
Internet Browser or Web Browser: A graphical interface tool that runs Internet protocols such as http, and displays results on the customers screen. The browser can act as an Internet tour guide, complete with pictorial desktops, directories and search tools used when a user “surfs” the Internet. In this application the Web browser is a client service which communicates with the World Wide Web.
Tissue: Any substance that contains material from which genetic information can be derived, resulting in a genetic profile, including but not limited to DNA, RNA, amino acids, single cells, portions of cells, multiple cells of the same type, or composite groups of cells of different types.
Genetic profile: A compilation of analyzed genetic data representing a tissue sample collected from a single person, animal, or plant, where specific values have been assigned for each allele analyzed.
Allele: An alternative form of a gene (one member of a pair) that is located at a specific position on a specific chromosome.
3. Description of Related Art
Genetic analysis is a multi step process. First a tissue sample is obtained, DNA is isolated, and the DNA is amplified using a process called PCR (Polymerase Chain Reaction). The PCR process results in millions to billions of copies of a specific segment of DNA. PCR can also be used to amplify RNA. PCR may or may not include the incorporation of a fluorescent tag within the segment. Amplified DNA must then be processed in one of several ways so as to create electronic data. There are many commercially available systems for processing PCR-amplified DNA products, including systems marketed by companies such as Promega Corporation and Applied Biosystems Incorporated (ABI). Once the amplified DNA has been processed and raw electronic data has been obtained, the data must then be analyzed to determine specific allele assignments for each DNA segment. Finally, the resulting genetic profile can be compared to other genetic profiles to verify identity, determine parentage, determine predisposition to disease, and for many other uses. These steps are described in more detail below.
There are two primary targets for the PCR process: STRs and SNPs. Both STRs and SNPs have been used extensively for various types of genetic analysis. Computer-implemented methods for discovering SNPs and determining genotypes are disclosed in, e.g., U.S. Pat. No. 5,858,659. While SNPs vary from individual to individual only in the sequence of the target DNA segment, STRs vary from individual to individual in the length and sequence of the target DNA segment. In either case the detectable differences between individuals in STR or SNP genetic profiles offer the opportunity to create a completely unique identification by DNA for each living creature on earth.
Fluorescently labeled STRs can be placed in a genetic analyzer that separates them on the basis of their size. Labeled SNPs can be detected by sequence specific primers of varying lengths which confer a size difference during PCR in the resulting DNA segment or by sequence specific probes such as affixed to a microarray. When dealing with segments of varying size, whether STR or SNP, conventional genetic analyzers use capillary electrophoresis to separate the segments by fragment size. A laser coupled with a photo-detector is then used to detect the amplified DNA segments of different sizes. An example of such a conventional system is the ABI 3730 Genetic Analyzer.
Typically, the output of a system such as the ABI3730 Genetic Analyzer is a raw data file for each sample which is stored electronically. Further analysis is required to convert the raw data to identifiable alleles for each DNA segment tested. The raw data can be imported into an analysis program such as ABI's GeneMapper. The GeneMapper program converts the raw data into an electropherogram which is a series of fluorescent peaks at varying sizes. By use of an internal standard common to every sample, the peaks are given a specific size, with one or two sizes or alleles detected at each DNA segment. A completed genetic profile consists of analyzed genetic data from a single tissue sample, where specific alleles have been assigned for each allele. At this point the genetic profile can be compared against other genetic profiles for several specific purposes.
One common use of genetic profiles is to confirm the parentage of an offspring.
For example, it is possible to identify the father of a child by testing the genetic of the mother, her child, and any number of potential fathers. Once tissue is obtained from the mother, the child, and the prospective fathers, genetic is isolated, processed, and analyzed to create genetic profiles for each individual. An analyst then compares the genetic profiles with each other. The genetic profile of the offspring must be a combination of the two actual parents. An allele in the offspring that cannot be attributed to one of the males excludes that male as a possible parent.
Another common use of genetic profiles is genetic matching. For example, a prized dog is stolen from a breeder's kennel. The breeder (breeder 1) suspects that another breeder (breeder 2) down the road now has her dog, but she can't prove it. She has tested her dog in the past and has his genetic profile stored. She obtains a tissue sample of the suspect dog and sends it to a lab for genetic analysis. The lab isolates and amplifies the genetic, as described above. The lab then creates a genetic profile for the suspect dog. Finally, an analyst compares the new genetic profile with the existing genetic profile. Identical genetic profiles serve as proof that the dog belongs to breeder 1.
Yet other uses of genetic profiles are trait detection and identifying predisposition to specific diseases. genetic segments that are amplified through the PCR process can be specified to genes that are associated with specific traits or diseases of interest. Typically, a consumer who wishes to know whether a subject has a certain trait or disease must submit a sample with personal information attached. Again, DNA is isolated and amplified, and a genetic profile is created. Again, an analyst must compare the genetic profile with profiles that are known to reflect association with the specific disease or trait of interest.
All of the current uses of genetic profiles require skilled analysts to perform comparisons of the genetic profiles after they have been produced. This requirement, that a skilled analyst perform all genetic profile comparisons, creates several limitations to the use of genetic analysis. Limited availability of skilled analysts creates delays in obtaining test results. Also, required use of skilled analysts for genetic profile comparisons reduces privacy for the consumer. Further, due to the current methods of genetic profile data storage skilled analysts often require new genetic profiles to be created prior to each comparison, even when an identical genetic profile has already been created for the individual being tested. This creates delays caused by unnecessary repetition in physical transport of tissue samples, data creation, and data processing. In other words, all the steps leading to production of a genetic profile for a given individual are unnecessarily repeated. Accordingly, there is a need for a computerized system that is accessible from anywhere in the world to store completed genetic profiles and to repeatedly perform specific genetic analyses at the direction of comparatively unskilled consumers, according to said consumer's specific inquiry, without the need to create new genetic profiles prior to each comparison.